load Brgo.v3.0anno.Atgoslim.BP.list
load(file.path("..","Annotation_copy","output","v3.0annotation","Brgo.v3.0anno.Atgoslim.BP.list.Rdata"))
load GO.ORA function
GOseq function for Brassica rapa (v3.0)
# GOseq
library(ShortRead);library(goseq);library(GO.db);library("annotate")
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## Welcome to Bioconductor
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## 'citation("Biobase")', and for packages 'citation("pkgname")'.
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## select
## Loading required package: XML
# for ggplot heatmap
## uncompress gz file
system(paste("gunzip -c ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.gz")," > ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")))
## read cDNA fasta file
Bra.v3.0_cdna<-readDNAStringSet(file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")) # copied from /Volumes/data_work/Data8/NGS_related/Brassica_rapa_Upendra/G3
Bra.v3.0_cdna
## A DNAStringSet instance of length 46250
## width seq names
## [1] 1254 ATGCGACCACCGGGTGTTGTT...GAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2] 1668 ATGCCAGCAATGCATGCCGTT...AGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3] 957 ATGATGCTTCTCGTTCATACC...AACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4] 1299 ATGAGTCGTCTTCTCCTTGCT...GGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5] 774 ATGGATTCTGGGCTTCAGCAT...GGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## ... ... ...
## [46246] 162 ATGCGTCCGTCCTCAGCTCCC...TCTTTGGTGGTCCGGTTCTAA BraAnng001840.3C
## [46247] 1455 ATGTCTAATCAAGGATCAGGA...ACAGGTTTGTTTAGGTGCTAA BraAnng001850.3C
## [46248] 1011 ATGGACAACGTAATTCTGAAA...TCAGGGAAGAAAAGCCCCTGA BraAnng006150.3C
## [46249] 870 ATGTTTCCAAGACGTACAAGG...AGCAGTTGTCCTTATAGTTAG BraAnng000040.3C
## [46250] 1338 ATGCCGCAACAATACTGGAAC...GGAGAGAACCTTATCTCCTGA BraAnng003440.3C
## remove fasta file
system(paste("rm ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa"),sep=""))
# GOseq function
GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA<-function(genelist,padjust=0.05,ontology="BP",custom.category.list=Brgo.v3.0anno.Atgoslim.BP.list,Br_cdna=Bra.v3.0_cdna) { # return GO enrichment table, padjus, padjust=0.05.
bias<-nchar(Br_cdna)
names(bias)<-names(Br_cdna)
TF<-(names(bias) %in% genelist)*1
names(TF)<-names(bias)
#print(TF)
pwf<-nullp(TF,bias.data=bias)
#print(pwf$DEgenes)
GO.pval <- goseq(pwf,gene2cat=custom.category.list,use_genes_without_cat=TRUE) # format became different in new goseq version (021111). Does not work (042716)
#GO.pval <- goseq(pwf,gene2cat=Brgo.DF3,use_genes_without_cat=TRUE) # format became different in new goseq version (021111)
#head(GO.pval)
if(ontology=="BP") {
GO.pval2<-subset(GO.pval,ontology=="BP")
} else if(ontology=="CC") {
GO.pval2<-subset(GO.pval,ontology=="CC")
} else {
GO.pval2<-subset(GO.pval,ontology=="MF")
}
GO.pval2$over_represented_padjust<-p.adjust(GO.pval2$over_represented_pvalue,method="BH")
if(GO.pval2$over_represented_padjust[1]>padjust) return("no enriched GO")
else {
enriched.GO<-GO.pval2[GO.pval2$over_represented_padjust<padjust,]
print("enriched.GO is")
print(enriched.GO)
## write Term and Definition
for(i in 1:dim(enriched.GO)[1]) {
if(is.null(Term(GOTERM[enriched.GO[i,"category"]]))) {next} else {
enriched.GO$Term[i]<-Term(GOTERM[[enriched.GO[i,"category"]]])
enriched.GO$Definition[i]<-Definition(GOTERM[[enriched.GO[i,"category"]]])
}
}
return(enriched.GO)
}
}
#
head(Bra.v3.0_cdna)
## A DNAStringSet instance of length 6
## width seq names
## [1] 1254 ATGCGACCACCGGGTGTTGTTTC...CTGAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2] 1668 ATGCCAGCAATGCATGCCGTTTT...GTAGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3] 957 ATGATGCTTCTCGTTCATACCCG...GGAACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4] 1299 ATGAGTCGTCTTCTCCTTGCTCA...GTGGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5] 774 ATGGATTCTGGGCTTCAGCATCT...AAGGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## [6] 3327 ATGGCGTCCACTCCTCCTCAAAA...GCGGTGGGTTTCAATTTCCTTGA BraA01g000060.3C
# length(bias) # 44239 > 45019 where the bias come from?
# bias.data vector must have the same length as DEgenes vector!
ORA: two afternoon trt and expression pattern
twoafternoon.trtlive.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.trtlive.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
## genes = col_character(),
## logFC = col_double(),
## logCPM = col_double(),
## LR = col_double(),
## PValue = col_double(),
## FDR = col_double(),
## AGI = col_character(),
## At_symbol = col_character(),
## At_short_description = col_character(),
## perc_ID = col_double()
## )
library(dplyr)
#genelist.up<-base::get(paste("../output/",DEG.objs.v3.0annotation.unique[n],sep="")) %>% rownames_to_column() %>% dplyr::filter(logFC>0) # does not work
temp<-twoafternoon.trtlive.DEGs.all.v3.0anno
genelist.up<-temp[temp[,"logFC"]>0&temp[,"FDR"]<0.05,"genes"];genelist.down<-temp[temp[,"logFC"]<0&temp[,"FDR"]<0.05,"genes"]
# check logFC value ()
temp[temp[,3]>0&temp[,3]<0.05,"logFC"] # previous version (before Feb 7, 2020)
temp[temp[,"logFC"]>0&temp[,"FDR"]<0.05,"logFC"] # revised version (after Feb 7, 2020)
print(paste("number of up genes is ",dim(genelist.up)[1]))
## [1] "number of up genes is 459"
# expression pattern of upregulated genes
gene.of.interest.FDR.up <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC>0) %>%
dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
print("logFC>0")
## [1] "logFC>0"
p.up1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[1,]);p.up1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[2,]);p.up2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[3,]);p.up3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[4,]);p.up4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[5,]);p.up5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
# expression pattern of diwbregulated genes
gene.of.interest.FDR.down <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC<0) %>% dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
print("logFC<0")
## [1] "logFC<0"
p.down1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[1,]);p.down1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[2,]);p.down2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[3,]);p.down3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[4,]);p.down4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[5,]);p.down5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
#genelist.down<-read_csv(paste("../output/",file,sep="")) %>% dplyr::filter(logFC.genotypeR500<0)
if(dim(genelist.up)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.up<-"no enriched GO";next} else {GO.ORA.temp.up<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.up)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
## [1] "enriched.GO is"
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 3164 GO:0071732 6.820561e-08 1.0000000 8
## 3114 GO:0071369 2.089131e-07 1.0000000 8
## 1195 GO:0010167 1.021437e-06 0.9999999 7
## 3094 GO:0071281 1.955280e-06 0.9999998 8
## 1530 GO:0016036 7.136493e-06 0.9999990 10
## 254 GO:0006096 2.202118e-05 0.9999970 9
## 1445 GO:0015706 8.135340e-05 0.9999948 5
## numInCat term ontology
## 3164 52 cellular response to nitric oxide BP
## 3114 62 cellular response to ethylene stimulus BP
## 1195 53 response to nitrate BP
## 3094 77 cellular response to iron ion BP
## 1530 148 cellular response to phosphate starvation BP
## 254 138 glycolytic process BP
## 1445 39 nitrate transport BP
## over_represented_padjust
## 3164 0.0002584311
## 3114 0.0003957859
## 1195 0.0012900754
## 3094 0.0018521386
## 1530 0.0054080343
## 254 0.0139063745
## 1445 0.0440354306
print(paste("number of down genes is ",dim(genelist.down)[1]))
## [1] "number of down genes is 1015"
if(dim(genelist.down)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.down<-"no enriched GO"; next} else {GO.ORA.temp.down<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.down)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
## [1] "enriched.GO is"
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200 4.504540e-16 1.0000000 35
## 2253 GO:0042742 5.385608e-14 1.0000000 56
## 638 GO:0006952 7.545274e-13 1.0000000 72
## 2750 GO:0050832 2.359748e-11 1.0000000 37
## 890 GO:0009611 5.566564e-11 1.0000000 36
## 3708 GO:2000022 2.000124e-10 1.0000000 16
## 899 GO:0009626 6.561878e-10 1.0000000 20
## 423 GO:0006468 2.148206e-09 1.0000000 81
## 853 GO:0009407 2.454257e-08 1.0000000 11
## 1166 GO:0010112 2.807664e-08 1.0000000 8
## 557 GO:0006749 1.255567e-07 1.0000000 12
## 894 GO:0009617 1.473423e-07 1.0000000 22
## 1174 GO:0010120 2.496944e-07 1.0000000 8
## 972 GO:0009751 4.766890e-07 0.9999999 25
## 900 GO:0009627 6.998144e-07 0.9999999 13
## 855 GO:0009409 1.752277e-06 0.9999993 37
## 1038 GO:0009871 3.976235e-06 0.9999999 5
## 1858 GO:0031348 5.987811e-06 0.9999992 10
## 1857 GO:0031347 8.866320e-06 0.9999986 11
## 646 GO:0006979 1.247452e-05 0.9999955 28
## 3442 GO:1900067 1.481476e-05 1.0000000 3
## 1183 GO:0010150 2.707898e-05 0.9999927 17
## 1107 GO:0010030 2.844214e-05 0.9999967 8
## 49 GO:0000272 3.213706e-05 0.9999970 7
## 2986 GO:0062034 3.975137e-05 0.9999991 4
## 2439 GO:0045332 4.455056e-05 0.9999967 6
## 185 GO:0002229 5.052194e-05 0.9999887 13
## 2859 GO:0051707 9.404250e-05 0.9999827 10
## 234 GO:0006032 9.606073e-05 0.9999914 6
## 1460 GO:0015749 1.074678e-04 0.9999934 5
## 478 GO:0006562 1.084541e-04 0.9999992 3
## 1291 GO:0010345 1.123459e-04 0.9999869 7
## 619 GO:0006887 1.685980e-04 0.9999666 10
## 921 GO:0009651 1.797603e-04 0.9999078 44
## 3251 GO:0080142 1.838731e-04 0.9999872 5
## 944 GO:0009697 1.865949e-04 0.9999867 5
## 859 GO:0009414 2.028253e-04 0.9999119 29
## 1001 GO:0009816 2.098586e-04 0.9999573 10
## 2617 GO:0048194 2.349755e-04 0.9999825 5
## 1177 GO:0010133 2.697046e-04 0.9999958 3
## 1030 GO:0009862 2.758968e-04 0.9999781 5
## 2247 GO:0042593 3.361831e-04 0.9999921 3
## 1002 GO:0009817 3.842136e-04 0.9999234 9
## 187 GO:0002237 4.003418e-04 0.9999202 9
## 2223 GO:0042344 4.121584e-04 0.9999773 4
## 1859 GO:0031349 4.498132e-04 0.9999756 4
## 2794 GO:0051258 5.343753e-04 0.9999875 3
## 2917 GO:0055114 5.773902e-04 0.9996410 71
## numInCat
## 1210 286
## 2253 726
## 638 1165
## 2750 469
## 890 419
## 3708 89
## 899 140
## 423 1484
## 853 67
## 1166 22
## 557 85
## 894 241
## 1174 27
## 972 347
## 900 104
## 855 696
## 1038 11
## 1858 64
## 1857 95
## 646 502
## 3442 3
## 1183 219
## 1107 54
## 49 39
## 2986 8
## 2439 23
## 185 126
## 2859 97
## 234 35
## 1460 18
## 478 4
## 1291 41
## 619 96
## 921 1045
## 3251 19
## 944 21
## 859 596
## 1001 97
## 2617 20
## 1177 5
## 1030 24
## 2247 8
## 1002 100
## 187 88
## 2223 15
## 1859 13
## 2794 6
## 2917 1923
## term
## 1210 response to chitin
## 2253 defense response to bacterium
## 638 defense response
## 2750 defense response to fungus
## 890 response to wounding
## 3708 regulation of jasmonic acid mediated signaling pathway
## 899 plant-type hypersensitive response
## 423 protein phosphorylation
## 853 toxin catabolic process
## 1166 regulation of systemic acquired resistance
## 557 glutathione metabolic process
## 894 response to bacterium
## 1174 camalexin biosynthetic process
## 972 response to salicylic acid
## 900 systemic acquired resistance
## 855 response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858 negative regulation of defense response
## 1857 regulation of defense response
## 646 response to oxidative stress
## 3442 regulation of cellular response to alkaline pH
## 1183 leaf senescence
## 1107 positive regulation of seed germination
## 49 polysaccharide catabolic process
## 2986 L-pipecolic acid biosynthetic process
## 2439 phospholipid translocation
## 185 defense response to oomycetes
## 2859 response to other organism
## 234 chitin catabolic process
## 1460 monosaccharide transmembrane transport
## 478 proline catabolic process
## 1291 suberin biosynthetic process
## 619 exocytosis
## 921 response to salt stress
## 3251 regulation of salicylic acid biosynthetic process
## 944 salicylic acid biosynthetic process
## 859 response to water deprivation
## 1001 defense response to bacterium, incompatible interaction
## 2617 Golgi vesicle budding
## 1177 proline catabolic process to glutamate
## 1030 systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247 glucose homeostasis
## 1002 defense response to fungus, incompatible interaction
## 187 response to molecule of bacterial origin
## 2223 indole glucosinolate catabolic process
## 1859 positive regulation of defense response
## 2794 protein polymerization
## 2917 oxidation-reduction process
## ontology over_represented_padjust
## 1210 BP 1.706770e-12
## 2253 BP 1.020303e-10
## 638 BP 9.529681e-10
## 2750 BP 2.235271e-08
## 890 BP 4.218342e-08
## 3708 BP 1.263079e-07
## 899 BP 3.551851e-07
## 423 BP 1.017444e-06
## 853 BP 1.033242e-05
## 1166 BP 1.063824e-05
## 557 BP 4.324859e-05
## 894 BP 4.652334e-05
## 1174 BP 7.277632e-05
## 972 BP 1.290125e-04
## 900 BP 1.767731e-04
## 855 BP 4.149611e-04
## 1038 BP 8.862326e-04
## 1858 BP 1.260434e-03
## 1857 BP 1.768131e-03
## 646 BP 2.363297e-03
## 3442 BP 2.673007e-03
## 1183 BP 4.663739e-03
## 1107 BP 4.685533e-03
## 49 BP 5.073638e-03
## 2986 BP 6.024717e-03
## 2439 BP 6.492387e-03
## 185 BP 7.089912e-03
## 2859 BP 1.255083e-02
## 234 BP 1.255083e-02
## 1460 BP 1.325589e-02
## 478 BP 1.325589e-02
## 1291 BP 1.330246e-02
## 619 BP 1.935812e-02
## 921 BP 1.963911e-02
## 3251 BP 1.963911e-02
## 944 BP 1.963911e-02
## 859 BP 2.077041e-02
## 1001 BP 2.092512e-02
## 2617 BP 2.282878e-02
## 1177 BP 2.549690e-02
## 1030 BP 2.549690e-02
## 2247 BP 3.032851e-02
## 1002 BP 3.385547e-02
## 187 BP 3.447489e-02
## 2223 BP 3.470374e-02
## 1859 BP 3.705092e-02
## 2794 BP 4.307975e-02
## 2917 BP 4.557774e-02
# handling "no enriched GO"
# genelist.names<-c("GO.ORA.temp.up_down","GO.ORA.temp.down_up") # test
x<-list(GO.ORA.up=GO.ORA.temp.up,
GO.ORA.down=GO.ORA.temp.down) # list
# x<-x[!x=="no enriched GO"] # remove "no enriched GO" result
## add sample info and FC info and save GO.ORA result
if(length(x)==0) {next} else {GO.ORA.result<-x}
GO.ORA.result
## $GO.ORA.up
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 3164 GO:0071732 6.820561e-08 1.0000000 8
## 3114 GO:0071369 2.089131e-07 1.0000000 8
## 1195 GO:0010167 1.021437e-06 0.9999999 7
## 3094 GO:0071281 1.955280e-06 0.9999998 8
## 1530 GO:0016036 7.136493e-06 0.9999990 10
## 254 GO:0006096 2.202118e-05 0.9999970 9
## 1445 GO:0015706 8.135340e-05 0.9999948 5
## numInCat term ontology
## 3164 52 cellular response to nitric oxide BP
## 3114 62 cellular response to ethylene stimulus BP
## 1195 53 response to nitrate BP
## 3094 77 cellular response to iron ion BP
## 1530 148 cellular response to phosphate starvation BP
## 254 138 glycolytic process BP
## 1445 39 nitrate transport BP
## over_represented_padjust Term
## 3164 0.0002584311 cellular response to nitric oxide
## 3114 0.0003957859 cellular response to ethylene stimulus
## 1195 0.0012900754 response to nitrate
## 3094 0.0018521386 cellular response to iron ion
## 1530 0.0054080343 cellular response to phosphate starvation
## 254 0.0139063745 glycolytic process
## 1445 0.0440354306 nitrate transport
## Definition
## 3164 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
## 3114 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethylene (ethene) stimulus.
## 1195 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrate stimulus.
## 3094 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
## 1530 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
## 254 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
## 1445 The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
##
## $GO.ORA.down
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200 4.504540e-16 1.0000000 35
## 2253 GO:0042742 5.385608e-14 1.0000000 56
## 638 GO:0006952 7.545274e-13 1.0000000 72
## 2750 GO:0050832 2.359748e-11 1.0000000 37
## 890 GO:0009611 5.566564e-11 1.0000000 36
## 3708 GO:2000022 2.000124e-10 1.0000000 16
## 899 GO:0009626 6.561878e-10 1.0000000 20
## 423 GO:0006468 2.148206e-09 1.0000000 81
## 853 GO:0009407 2.454257e-08 1.0000000 11
## 1166 GO:0010112 2.807664e-08 1.0000000 8
## 557 GO:0006749 1.255567e-07 1.0000000 12
## 894 GO:0009617 1.473423e-07 1.0000000 22
## 1174 GO:0010120 2.496944e-07 1.0000000 8
## 972 GO:0009751 4.766890e-07 0.9999999 25
## 900 GO:0009627 6.998144e-07 0.9999999 13
## 855 GO:0009409 1.752277e-06 0.9999993 37
## 1038 GO:0009871 3.976235e-06 0.9999999 5
## 1858 GO:0031348 5.987811e-06 0.9999992 10
## 1857 GO:0031347 8.866320e-06 0.9999986 11
## 646 GO:0006979 1.247452e-05 0.9999955 28
## 3442 GO:1900067 1.481476e-05 1.0000000 3
## 1183 GO:0010150 2.707898e-05 0.9999927 17
## 1107 GO:0010030 2.844214e-05 0.9999967 8
## 49 GO:0000272 3.213706e-05 0.9999970 7
## 2986 GO:0062034 3.975137e-05 0.9999991 4
## 2439 GO:0045332 4.455056e-05 0.9999967 6
## 185 GO:0002229 5.052194e-05 0.9999887 13
## 2859 GO:0051707 9.404250e-05 0.9999827 10
## 234 GO:0006032 9.606073e-05 0.9999914 6
## 1460 GO:0015749 1.074678e-04 0.9999934 5
## 478 GO:0006562 1.084541e-04 0.9999992 3
## 1291 GO:0010345 1.123459e-04 0.9999869 7
## 619 GO:0006887 1.685980e-04 0.9999666 10
## 921 GO:0009651 1.797603e-04 0.9999078 44
## 3251 GO:0080142 1.838731e-04 0.9999872 5
## 944 GO:0009697 1.865949e-04 0.9999867 5
## 859 GO:0009414 2.028253e-04 0.9999119 29
## 1001 GO:0009816 2.098586e-04 0.9999573 10
## 2617 GO:0048194 2.349755e-04 0.9999825 5
## 1177 GO:0010133 2.697046e-04 0.9999958 3
## 1030 GO:0009862 2.758968e-04 0.9999781 5
## 2247 GO:0042593 3.361831e-04 0.9999921 3
## 1002 GO:0009817 3.842136e-04 0.9999234 9
## 187 GO:0002237 4.003418e-04 0.9999202 9
## 2223 GO:0042344 4.121584e-04 0.9999773 4
## 1859 GO:0031349 4.498132e-04 0.9999756 4
## 2794 GO:0051258 5.343753e-04 0.9999875 3
## 2917 GO:0055114 5.773902e-04 0.9996410 71
## numInCat
## 1210 286
## 2253 726
## 638 1165
## 2750 469
## 890 419
## 3708 89
## 899 140
## 423 1484
## 853 67
## 1166 22
## 557 85
## 894 241
## 1174 27
## 972 347
## 900 104
## 855 696
## 1038 11
## 1858 64
## 1857 95
## 646 502
## 3442 3
## 1183 219
## 1107 54
## 49 39
## 2986 8
## 2439 23
## 185 126
## 2859 97
## 234 35
## 1460 18
## 478 4
## 1291 41
## 619 96
## 921 1045
## 3251 19
## 944 21
## 859 596
## 1001 97
## 2617 20
## 1177 5
## 1030 24
## 2247 8
## 1002 100
## 187 88
## 2223 15
## 1859 13
## 2794 6
## 2917 1923
## term
## 1210 response to chitin
## 2253 defense response to bacterium
## 638 defense response
## 2750 defense response to fungus
## 890 response to wounding
## 3708 regulation of jasmonic acid mediated signaling pathway
## 899 plant-type hypersensitive response
## 423 protein phosphorylation
## 853 toxin catabolic process
## 1166 regulation of systemic acquired resistance
## 557 glutathione metabolic process
## 894 response to bacterium
## 1174 camalexin biosynthetic process
## 972 response to salicylic acid
## 900 systemic acquired resistance
## 855 response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858 negative regulation of defense response
## 1857 regulation of defense response
## 646 response to oxidative stress
## 3442 regulation of cellular response to alkaline pH
## 1183 leaf senescence
## 1107 positive regulation of seed germination
## 49 polysaccharide catabolic process
## 2986 L-pipecolic acid biosynthetic process
## 2439 phospholipid translocation
## 185 defense response to oomycetes
## 2859 response to other organism
## 234 chitin catabolic process
## 1460 monosaccharide transmembrane transport
## 478 proline catabolic process
## 1291 suberin biosynthetic process
## 619 exocytosis
## 921 response to salt stress
## 3251 regulation of salicylic acid biosynthetic process
## 944 salicylic acid biosynthetic process
## 859 response to water deprivation
## 1001 defense response to bacterium, incompatible interaction
## 2617 Golgi vesicle budding
## 1177 proline catabolic process to glutamate
## 1030 systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247 glucose homeostasis
## 1002 defense response to fungus, incompatible interaction
## 187 response to molecule of bacterial origin
## 2223 indole glucosinolate catabolic process
## 1859 positive regulation of defense response
## 2794 protein polymerization
## 2917 oxidation-reduction process
## ontology over_represented_padjust
## 1210 BP 1.706770e-12
## 2253 BP 1.020303e-10
## 638 BP 9.529681e-10
## 2750 BP 2.235271e-08
## 890 BP 4.218342e-08
## 3708 BP 1.263079e-07
## 899 BP 3.551851e-07
## 423 BP 1.017444e-06
## 853 BP 1.033242e-05
## 1166 BP 1.063824e-05
## 557 BP 4.324859e-05
## 894 BP 4.652334e-05
## 1174 BP 7.277632e-05
## 972 BP 1.290125e-04
## 900 BP 1.767731e-04
## 855 BP 4.149611e-04
## 1038 BP 8.862326e-04
## 1858 BP 1.260434e-03
## 1857 BP 1.768131e-03
## 646 BP 2.363297e-03
## 3442 BP 2.673007e-03
## 1183 BP 4.663739e-03
## 1107 BP 4.685533e-03
## 49 BP 5.073638e-03
## 2986 BP 6.024717e-03
## 2439 BP 6.492387e-03
## 185 BP 7.089912e-03
## 2859 BP 1.255083e-02
## 234 BP 1.255083e-02
## 1460 BP 1.325589e-02
## 478 BP 1.325589e-02
## 1291 BP 1.330246e-02
## 619 BP 1.935812e-02
## 921 BP 1.963911e-02
## 3251 BP 1.963911e-02
## 944 BP 1.963911e-02
## 859 BP 2.077041e-02
## 1001 BP 2.092512e-02
## 2617 BP 2.282878e-02
## 1177 BP 2.549690e-02
## 1030 BP 2.549690e-02
## 2247 BP 3.032851e-02
## 1002 BP 3.385547e-02
## 187 BP 3.447489e-02
## 2223 BP 3.470374e-02
## 1859 BP 3.705092e-02
## 2794 BP 4.307975e-02
## 2917 BP 4.557774e-02
## Term
## 1210 response to chitin
## 2253 defense response to bacterium
## 638 defense response
## 2750 defense response to fungus
## 890 response to wounding
## 3708 regulation of jasmonic acid mediated signaling pathway
## 899 plant-type hypersensitive response
## 423 protein phosphorylation
## 853 toxin catabolic process
## 1166 regulation of systemic acquired resistance
## 557 glutathione metabolic process
## 894 response to bacterium
## 1174 camalexin biosynthetic process
## 972 response to salicylic acid
## 900 systemic acquired resistance
## 855 response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858 negative regulation of defense response
## 1857 regulation of defense response
## 646 response to oxidative stress
## 3442 regulation of cellular response to alkaline pH
## 1183 leaf senescence
## 1107 positive regulation of seed germination
## 49 polysaccharide catabolic process
## 2986 L-pipecolic acid biosynthetic process
## 2439 phospholipid translocation
## 185 defense response to oomycetes
## 2859 response to other organism
## 234 chitin catabolic process
## 1460 monosaccharide transmembrane transport
## 478 proline catabolic process
## 1291 suberin biosynthetic process
## 619 exocytosis
## 921 response to salt stress
## 3251 regulation of salicylic acid biosynthetic process
## 944 salicylic acid biosynthetic process
## 859 response to water deprivation
## 1001 defense response to bacterium, incompatible interaction
## 2617 Golgi vesicle budding
## 1177 proline catabolic process to glutamate
## 1030 systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247 glucose homeostasis
## 1002 defense response to fungus, incompatible interaction
## 187 response to molecule of bacterial origin
## 2223 indole glucosinolate catabolic process
## 1859 positive regulation of defense response
## 2794 protein polymerization
## 2917 oxidation-reduction process
## Definition
## 1210 A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.
## 2253 Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
## 638 Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
## 2750 Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
## 890 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
## 3708 Any process that modulates the frequency, rate or extent of jasmonic acid mediated signaling pathway.
## 899 The rapid, localized death of plant cells in response to invasion by a pathogen.
## 423 The process of introducing a phosphate group on to a protein.
## 853 The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
## 1166 Any process that modulates the frequency, rate or extent of systemic acquired resistance.
## 557 The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
## 894 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
## 1174 The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
## 972 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
## 900 The salicylic acid mediated response to a pathogen which confers broad spectrum resistance.
## 855 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
## 1038 The series of molecular signals mediated by ethylene (ethene) involved in jasmonic acid/ethylene dependent systemic resistance.
## 1858 Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response.
## 1857 Any process that modulates the frequency, rate or extent of a defense response.
## 646 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
## 3442 <NA>
## 1183 The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.
## 1107 Any process that activates or increase the rate of seed germination.
## 49 The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
## 2986 The chemical reactions and pathways resulting in the formation of L-pipecolic acid, a metabolite of lysine.
## 2439 The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.
## 185 Reactions triggered in response to the presence of oomycetes that act to protect the cell or organism.
## 2859 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
## 234 The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
## 1460 The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
## 478 The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
## 1291 The chemical reactions and pathways resulting in the formation of suberin monomers and suberin polyesters. Suberin monomers are derived from fatty acids and trans-cinnamic acids. The monomers are then cross-linked with glycerols.
## 619 A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
## 921 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
## 3251 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of salicylic acid.
## 944 The chemical reactions and pathways resulting in the formation of salicylic acid (2-hydroxybenzoic acid), a derivative of benzoic acid.
## 859 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.
## 1001 A response of an organism to a bacterium that prevents the occurrence or spread of disease.
## 2617 The evagination of the Golgi membrane, resulting in formation of a vesicle.
## 1177 The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.
## 1030 The series of molecular signals mediated by salicylic acid involved in systemic acquired resistance.
## 2247 Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
## 1002 A response of an organism to a fungus that prevents the occurrence or spread of disease.
## 187 Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
## 2223 The chemical reactions and pathways resulting in the breakdown of indole glucosinolates, sulfur-containing compounds that have a common structure linked to an R group derived from tryptophan.
## 1859 Any process that activates or increases the frequency, rate or extent of a defense response.
## 2794 The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
## 2917 A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
# GO.ORA.result %>% bind_rows() %>% View()
GO.ORA.result.DF <- GO.ORA.result%>% enframe() %>% unnest(value) # %>% View()
# save data
# save(GO.ORA.result,file="../output/GOseq.timecourse.twoafternoon.Brgo.v3.0.Atgoslim.BP.list.enrich.Rdata")
write_csv(GO.ORA.result.DF, path=file.path("..","output","twoafternoon.trtlive.DEGs.GO.ORA.v3.0anno.csv"))
ORA: two afternoon interaction only and expression pattern
twoafternoon.interaction.trtlive.samplingday.lrt.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.interaction.trtlive.samplingday.lrt.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
## genes = col_character(),
## logFC.soil_trtSBC_OLD.sampling_day03 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day04 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day06 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day08 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day10 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day13 = col_double(),
## logFC.soil_trtSBC_OLD.sampling_day14 = col_double(),
## logCPM = col_double(),
## LR = col_double(),
## PValue = col_double(),
## FDR = col_double(),
## AGI = col_character(),
## At_symbol = col_character(),
## At_short_description = col_character(),
## perc_ID = col_double()
## )
library(dplyr)
#genelist.up<-base::get(paste("../output/",DEG.objs.v3.0annotation.unique[n],sep="")) %>% rownames_to_column() %>% dplyr::filter(logFC>0) # does not work
temp<-twoafternoon.trtlive.DEGs.all.v3.0anno
genelist<-temp[temp[,"FDR"]<0.05,"genes"]
print(paste("number of up genes is ",dim(genelist)[1]))
## [1] "number of up genes is 1474"
# expression pattern
gene.of.interest.FDR <- twoafternoon.interaction.trtlive.samplingday.lrt.DEGs.all.v3.0anno %>% filter(FDR< 0.05) %>%
dplyr::select(genes,FDR) %>% arrange(FDR)
p1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[1,]);p1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[2,]);p2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[3,]);p3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[4,]);p4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[5,]);p5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
#genelist.down<-read_csv(paste("../output/",file,sep="")) %>% dplyr::filter(logFC.genotypeR500<0)
if(dim(genelist)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp<-"no enriched GO";next} else {GO.ORA.temp<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
## [1] "enriched.GO is"
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200 4.095158e-12 1.0000000 36
## 2253 GO:0042742 1.579177e-10 1.0000000 62
## 890 GO:0009611 2.727471e-09 1.0000000 41
## 638 GO:0006952 9.236316e-09 1.0000000 80
## 3708 GO:2000022 3.808132e-08 1.0000000 16
## 899 GO:0009626 5.899027e-08 1.0000000 21
## 2750 GO:0050832 6.644975e-08 1.0000000 39
## 1166 GO:0010112 4.664472e-07 1.0000000 8
## 853 GO:0009407 1.147806e-06 0.9999999 11
## 900 GO:0009627 1.596539e-06 0.9999997 15
## 646 GO:0006979 1.708851e-06 0.9999993 38
## 1174 GO:0010120 3.844295e-06 0.9999997 8
## 423 GO:0006468 3.882556e-06 0.9999980 94
## 894 GO:0009617 5.522889e-06 0.9999983 24
## 557 GO:0006749 6.475601e-06 0.9999989 12
## 855 GO:0009409 1.353825e-05 0.9999938 45
## 898 GO:0009625 1.847506e-05 0.9999966 12
## 1038 GO:0009871 2.347250e-05 0.9999991 5
## 2859 GO:0051707 2.416467e-05 0.9999951 13
## 2439 GO:0045332 3.325811e-05 0.9999971 7
## 972 GO:0009751 3.674037e-05 0.9999862 27
## 3442 GO:1900067 4.456149e-05 1.0000000 3
## 1857 GO:0031347 5.629769e-05 0.9999883 12
## 1107 GO:0010030 6.202572e-05 0.9999907 9
## 3164 GO:0071732 7.229820e-05 0.9999890 9
## 1183 GO:0010150 9.353298e-05 0.9999690 20
## 2617 GO:0048194 1.285276e-04 0.9999889 6
## 1858 GO:0031348 1.301439e-04 0.9999757 10
## 2986 GO:0062034 1.614913e-04 0.9999947 4
## 3114 GO:0071369 1.777013e-04 0.9999690 9
## 2917 GO:0055114 1.842612e-04 0.9998808 99
## 607 GO:0006869 2.458597e-04 0.9999269 15
## 478 GO:0006562 3.131506e-04 0.9999965 3
## 49 GO:0000272 3.172743e-04 0.9999562 7
## 1002 GO:0009817 3.721528e-04 0.9999113 11
## numInCat
## 1210 286
## 2253 726
## 890 419
## 638 1165
## 3708 89
## 899 140
## 2750 469
## 1166 22
## 853 67
## 900 104
## 646 502
## 1174 27
## 423 1484
## 894 241
## 557 85
## 855 696
## 898 84
## 1038 11
## 2859 97
## 2439 23
## 972 347
## 3442 3
## 1857 95
## 1107 54
## 3164 52
## 1183 219
## 2617 20
## 1858 64
## 2986 8
## 3114 62
## 2917 1923
## 607 208
## 478 4
## 49 39
## 1002 100
## term
## 1210 response to chitin
## 2253 defense response to bacterium
## 890 response to wounding
## 638 defense response
## 3708 regulation of jasmonic acid mediated signaling pathway
## 899 plant-type hypersensitive response
## 2750 defense response to fungus
## 1166 regulation of systemic acquired resistance
## 853 toxin catabolic process
## 900 systemic acquired resistance
## 646 response to oxidative stress
## 1174 camalexin biosynthetic process
## 423 protein phosphorylation
## 894 response to bacterium
## 557 glutathione metabolic process
## 855 response to cold
## 898 response to insect
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 2859 response to other organism
## 2439 phospholipid translocation
## 972 response to salicylic acid
## 3442 regulation of cellular response to alkaline pH
## 1857 regulation of defense response
## 1107 positive regulation of seed germination
## 3164 cellular response to nitric oxide
## 1183 leaf senescence
## 2617 Golgi vesicle budding
## 1858 negative regulation of defense response
## 2986 L-pipecolic acid biosynthetic process
## 3114 cellular response to ethylene stimulus
## 2917 oxidation-reduction process
## 607 lipid transport
## 478 proline catabolic process
## 49 polysaccharide catabolic process
## 1002 defense response to fungus, incompatible interaction
## ontology over_represented_padjust
## 1210 BP 1.551655e-08
## 2253 BP 2.991750e-07
## 890 BP 3.444795e-06
## 638 BP 8.749100e-06
## 3708 BP 2.885803e-05
## 899 BP 3.596830e-05
## 2750 BP 3.596830e-05
## 1166 BP 2.209211e-04
## 853 BP 4.832263e-04
## 900 BP 5.886216e-04
## 646 BP 5.886216e-04
## 1174 BP 1.131616e-03
## 423 BP 1.131616e-03
## 894 BP 1.494730e-03
## 557 BP 1.635737e-03
## 855 BP 3.206028e-03
## 898 BP 4.117764e-03
## 1038 BP 4.818943e-03
## 2859 BP 4.818943e-03
## 2439 BP 6.300748e-03
## 972 BP 6.629012e-03
## 3442 BP 7.674704e-03
## 1857 BP 9.274433e-03
## 1107 BP 9.792310e-03
## 3164 BP 1.095752e-02
## 1183 BP 1.363063e-02
## 2617 BP 1.761126e-02
## 1858 BP 1.761126e-02
## 2986 BP 2.109967e-02
## 3114 BP 2.244367e-02
## 2917 BP 2.252148e-02
## 607 BP 2.911133e-02
## 478 BP 3.535742e-02
## 49 BP 3.535742e-02
## 1002 BP 4.028820e-02
write_csv(GO.ORA.temp, path=file.path("..","output","twoafternoon.interaction.trtlive.samplingday.DEGs.GO.ORA.v3.0anno.csv"))
ORA: two afternoon trt + interaction only and expression pattern
twoafternoon.any.trtlive.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.any.trtlive.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
## genes = col_character(),
## logFC.sampling_day03 = col_double(),
## logFC.sampling_day04 = col_double(),
## logFC.sampling_day06 = col_double(),
## logFC.sampling_day08 = col_double(),
## logFC.sampling_day10 = col_double(),
## logFC.sampling_day13 = col_double(),
## logFC.sampling_day14 = col_double(),
## logCPM = col_double(),
## LR = col_double(),
## PValue = col_double(),
## FDR = col_double(),
## AGI = col_character(),
## At_symbol = col_character(),
## At_short_description = col_character(),
## perc_ID = col_double()
## )
temp<-twoafternoon.any.trtlive.DEGs.all.v3.0anno
genelist<-temp[temp[,"FDR"]<0.05,"genes"]
print(paste("number of up genes is ",dim(genelist)[1]))
## [1] "number of up genes is 15376"
# expression pattern
gene.of.interest.FDR <- twoafternoon.any.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05) %>%
dplyr::select(genes,FDR) %>% arrange(FDR)
p1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[1,]);p1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[2,]);p2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[3,]);p3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[4,]);p4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR[5,]);p5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
if(dim(genelist)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp<-"no enriched GO";next} else {
GO.ORA.temp<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist))
}
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
## [1] "enriched.GO is"
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 390 GO:0006412 2.513901e-76 1.0000000 417
## 921 GO:0009651 2.165836e-38 1.0000000 566
## 2575 GO:0046686 8.729195e-23 1.0000000 395
## 2211 GO:0042254 4.407992e-20 1.0000000 127
## 859 GO:0009414 5.762949e-20 1.0000000 315
## 854 GO:0009408 2.798669e-19 1.0000000 181
## 960 GO:0009737 5.874027e-16 1.0000000 402
## 646 GO:0006979 3.842850e-15 1.0000000 253
## 2917 GO:0055114 1.865078e-14 1.0000000 849
## 855 GO:0009409 1.975804e-14 1.0000000 330
## 359 GO:0006355 1.391844e-11 1.0000000 1189
## 2088 GO:0034605 1.504203e-11 1.0000000 77
## 958 GO:0009735 1.183400e-10 1.0000000 201
## 419 GO:0006457 1.333500e-10 1.0000000 205
## 178 GO:0002181 1.406214e-10 1.0000000 49
## 2253 GO:0042742 4.110520e-10 1.0000000 341
## 890 GO:0009611 4.640262e-10 1.0000000 210
## 3270 GO:0080167 5.448245e-10 1.0000000 134
## 642 GO:0006970 1.554491e-09 1.0000000 134
## 2239 GO:0042542 3.044208e-09 1.0000000 75
## 1210 GO:0010200 7.192915e-09 1.0000000 142
## 2152 GO:0035556 8.282079e-09 1.0000000 168
## 8 GO:0000027 1.949066e-08 1.0000000 44
## 894 GO:0009617 3.028600e-08 1.0000000 127
## 392 GO:0006414 3.900309e-08 1.0000000 62
## 1008 GO:0009826 1.137540e-07 1.0000000 134
## 2646 GO:0048364 1.237742e-07 1.0000000 167
## 1183 GO:0010150 2.248077e-07 1.0000000 114
## 3708 GO:2000022 3.049337e-07 0.9999999 54
## 972 GO:0009751 6.702788e-07 1.0000000 160
## 2254 GO:0042744 8.537941e-07 0.9999996 81
## 853 GO:0009407 8.721278e-07 0.9999998 38
## 914 GO:0009644 9.815138e-07 0.9999996 61
## 9 GO:0000028 1.339666e-06 0.9999996 34
## 2768 GO:0051085 1.696591e-06 0.9999994 50
## 1327 GO:0010411 2.116743e-06 0.9999993 48
## 557 GO:0006749 2.424669e-06 0.9999992 47
## 973 GO:0009753 4.575015e-06 0.9999977 157
## 967 GO:0009744 4.983374e-06 0.9999978 72
## 952 GO:0009723 5.460473e-06 0.9999974 122
## 1087 GO:0009970 6.394732e-06 0.9999994 19
## 739 GO:0007623 8.108282e-06 0.9999959 94
## 1530 GO:0016036 9.354672e-06 0.9999956 84
## 961 GO:0009738 1.043318e-05 0.9999937 198
## 3255 GO:0080147 1.231773e-05 0.9999971 28
## 2716 GO:0048767 1.294488e-05 0.9999948 57
## 3251 GO:0080142 1.488489e-05 0.9999989 17
## 153 GO:0001666 1.619553e-05 0.9999940 49
## 649 GO:0006986 1.875522e-05 0.9999967 24
## 423 GO:0006468 2.030599e-05 0.9999841 657
## 1737 GO:0019761 2.068416e-05 0.9999930 43
## 898 GO:0009625 2.208400e-05 0.9999916 47
## 2091 GO:0034620 2.507802e-05 0.9999943 27
## 2487 GO:0045893 2.555948e-05 0.9999826 241
## 2913 GO:0055085 2.825093e-05 0.9999807 270
## 594 GO:0006833 5.088514e-05 0.9999886 23
## 1205 GO:0010193 6.063073e-05 0.9999809 33
## 676 GO:0007043 6.756895e-05 0.9999957 10
## 1166 GO:0010112 7.427518e-05 0.9999891 17
## 3252 GO:0080143 7.827289e-05 0.9999941 9
## 3217 GO:0080037 7.909464e-05 0.9999966 11
## 1174 GO:0010120 8.907454e-05 0.9999834 20
## 2196 GO:0042026 9.201446e-05 0.9999600 52
## 607 GO:0006869 9.847090e-05 0.9999455 82
## 2795 GO:0051259 9.995934e-05 0.9999835 14
## 992 GO:0009800 1.061107e-04 1.0000000 10
## 985 GO:0009787 1.098167e-04 0.9999747 23
## 1760 GO:0030001 1.114888e-04 0.9999453 64
## 1001 GO:0009816 1.127544e-04 0.9999504 55
## 3546 GO:1902347 1.237733e-04 1.0000000 11
## 602 GO:0006855 1.255455e-04 0.9999378 74
## 1003 GO:0009819 1.275301e-04 0.9999780 18
## 2241 GO:0042546 1.357358e-04 0.9999403 51
## 452 GO:0006520 1.438881e-04 0.9999379 51
## 957 GO:0009734 1.515406e-04 0.9999001 161
## 87 GO:0000463 1.627838e-04 0.9999710 16
## 2679 GO:0048527 1.668161e-04 0.9999249 50
## 1116 GO:0010043 1.677154e-04 0.9999298 44
## 861 GO:0009416 1.680664e-04 0.9998877 174
## 91 GO:0000470 1.836594e-04 0.9999626 17
## 32 GO:0000162 2.034271e-04 0.9999482 24
## 3747 GO:2000306 2.434559e-04 0.9999891 9
## 2750 GO:0050832 2.519962e-04 0.9998246 192
## 636 GO:0006949 2.640376e-04 0.9999465 17
## 2259 GO:0042761 4.208985e-04 0.9998964 20
## 2973 GO:0061408 4.256525e-04 0.9998578 28
## 26 GO:0000103 4.366330e-04 0.9999112 17
## 1422 GO:0010942 4.650260e-04 0.9999430 13
## 1072 GO:0009955 4.807824e-04 0.9999569 11
## 748 GO:0008202 5.221926e-04 0.9998809 19
## 899 GO:0009626 5.278762e-04 0.9997147 72
## 2908 GO:0055073 5.495436e-04 1.0000000 5
## 897 GO:0009624 5.563898e-04 0.9996779 87
## 1030 GO:0009862 5.892519e-04 0.9998762 17
## 634 GO:0006914 6.115633e-04 0.9997652 32
## 2301 GO:0043069 6.195394e-04 0.9998401 19
## 203 GO:0003400 6.672923e-04 0.9999646 9
## 793 GO:0009098 6.841475e-04 0.9998234 20
## 2486 GO:0045892 6.884630e-04 0.9995310 152
## 1031 GO:0009863 7.091159e-04 0.9997831 24
## 2237 GO:0042538 7.202583e-04 0.9996160 60
## 910 GO:0009640 7.304979e-04 0.9996102 64
## 736 GO:0007568 7.436470e-04 0.9996590 42
## 930 GO:0009664 7.802128e-04 0.9996299 47
## 2889 GO:0052544 7.830832e-04 0.9997955 22
## 291 GO:0006207 8.882380e-04 0.9998429 14
## 1173 GO:0010119 9.290823e-04 0.9995077 62
## 2526 GO:0046274 9.944056e-04 0.9997488 21
## 860 GO:0009415 1.044018e-03 0.9998658 9
## 1671 GO:0019344 1.050348e-03 0.9996507 25
## 2964 GO:0061024 1.067505e-03 1.0000000 6
## 269 GO:0006120 1.131954e-03 0.9997453 13
## 1125 GO:0010053 1.146115e-03 0.9996112 26
## 2848 GO:0051603 1.211855e-03 0.9993065 72
## 516 GO:0006633 1.222438e-03 0.9992672 83
## 1380 GO:0010583 1.274437e-03 0.9994483 37
## 2831 GO:0051513 1.385094e-03 1.0000000 8
## 2214 GO:0042273 1.402079e-03 0.9995883 18
## 1916 GO:0032259 1.453590e-03 0.9990018 143
## 774 GO:0009058 1.490785e-03 0.9991314 77
## 1769 GO:0030042 1.557542e-03 0.9996215 14
## numInCat
## 390 715
## 921 1045
## 2575 753
## 2211 236
## 859 596
## 854 305
## 960 832
## 646 502
## 2917 1923
## 855 696
## 359 2992
## 2088 117
## 958 412
## 419 423
## 178 83
## 2253 726
## 890 419
## 3270 254
## 642 252
## 2239 130
## 1210 286
## 2152 313
## 8 72
## 894 241
## 392 105
## 1008 256
## 2646 326
## 1183 219
## 3708 89
## 972 347
## 2254 146
## 853 67
## 914 109
## 9 61
## 2768 82
## 1327 77
## 557 85
## 973 338
## 967 136
## 952 255
## 1087 22
## 739 181
## 1530 148
## 961 437
## 3255 42
## 2716 99
## 3251 19
## 153 83
## 649 31
## 423 1484
## 1737 69
## 898 84
## 2091 38
## 2487 570
## 2913 562
## 594 34
## 1205 54
## 676 12
## 1166 22
## 3252 12
## 3217 12
## 1174 27
## 2196 97
## 607 208
## 2795 22
## 992 10
## 985 33
## 1760 130
## 1001 97
## 3546 11
## 602 130
## 1003 24
## 2241 95
## 452 90
## 957 377
## 87 23
## 2679 99
## 1116 83
## 861 394
## 91 26
## 32 35
## 3747 10
## 2750 469
## 636 25
## 2259 30
## 2973 47
## 26 24
## 1422 16
## 1072 13
## 748 27
## 899 140
## 2908 5
## 897 176
## 1030 24
## 634 58
## 2301 30
## 203 10
## 793 30
## 2486 355
## 1031 38
## 2237 132
## 910 129
## 736 85
## 930 91
## 2889 31
## 291 19
## 1173 121
## 2526 29
## 860 13
## 1671 41
## 2964 6
## 269 23
## 1125 42
## 2848 151
## 516 180
## 1380 67
## 2831 8
## 2214 32
## 1916 324
## 774 154
## 1769 24
## term
## 390 translation
## 921 response to salt stress
## 2575 response to cadmium ion
## 2211 ribosome biogenesis
## 859 response to water deprivation
## 854 response to heat
## 960 response to abscisic acid
## 646 response to oxidative stress
## 2917 oxidation-reduction process
## 855 response to cold
## 359 regulation of transcription, DNA-templated
## 2088 cellular response to heat
## 958 response to cytokinin
## 419 protein folding
## 178 cytoplasmic translation
## 2253 defense response to bacterium
## 890 response to wounding
## 3270 response to karrikin
## 642 response to osmotic stress
## 2239 response to hydrogen peroxide
## 1210 response to chitin
## 2152 intracellular signal transduction
## 8 ribosomal large subunit assembly
## 894 response to bacterium
## 392 translational elongation
## 1008 unidimensional cell growth
## 2646 root development
## 1183 leaf senescence
## 3708 regulation of jasmonic acid mediated signaling pathway
## 972 response to salicylic acid
## 2254 hydrogen peroxide catabolic process
## 853 toxin catabolic process
## 914 response to high light intensity
## 9 ribosomal small subunit assembly
## 2768 chaperone cofactor-dependent protein refolding
## 1327 xyloglucan metabolic process
## 557 glutathione metabolic process
## 973 response to jasmonic acid
## 967 response to sucrose
## 952 response to ethylene
## 1087 cellular response to sulfate starvation
## 739 circadian rhythm
## 1530 cellular response to phosphate starvation
## 961 abscisic acid-activated signaling pathway
## 3255 root hair cell development
## 2716 root hair elongation
## 3251 regulation of salicylic acid biosynthetic process
## 153 response to hypoxia
## 649 response to unfolded protein
## 423 protein phosphorylation
## 1737 glucosinolate biosynthetic process
## 898 response to insect
## 2091 cellular response to unfolded protein
## 2487 positive regulation of transcription, DNA-templated
## 2913 transmembrane transport
## 594 water transport
## 1205 response to ozone
## 676 cell-cell junction assembly
## 1166 regulation of systemic acquired resistance
## 3252 regulation of amino acid export
## 3217 negative regulation of cytokinin-activated signaling pathway
## 1174 camalexin biosynthetic process
## 2196 protein refolding
## 607 lipid transport
## 2795 protein complex oligomerization
## 992 cinnamic acid biosynthetic process
## 985 regulation of abscisic acid-activated signaling pathway
## 1760 metal ion transport
## 1001 defense response to bacterium, incompatible interaction
## 3546 response to strigolactone
## 602 drug transmembrane transport
## 1003 drought recovery
## 2241 cell wall biogenesis
## 452 cellular amino acid metabolic process
## 957 auxin-activated signaling pathway
## 87 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
## 2679 lateral root development
## 1116 response to zinc ion
## 861 response to light stimulus
## 91 maturation of LSU-rRNA
## 32 tryptophan biosynthetic process
## 3747 positive regulation of photomorphogenesis
## 2750 defense response to fungus
## 636 syncytium formation
## 2259 very long-chain fatty acid biosynthetic process
## 2973 positive regulation of transcription from RNA polymerase II promoter in response to heat stress
## 26 sulfate assimilation
## 1422 positive regulation of cell death
## 1072 adaxial/abaxial pattern specification
## 748 steroid metabolic process
## 899 plant-type hypersensitive response
## 2908 cadmium ion homeostasis
## 897 response to nematode
## 1030 systemic acquired resistance, salicylic acid mediated signaling pathway
## 634 autophagy
## 2301 negative regulation of programmed cell death
## 203 regulation of COPII vesicle coating
## 793 leucine biosynthetic process
## 2486 negative regulation of transcription, DNA-templated
## 1031 salicylic acid mediated signaling pathway
## 2237 hyperosmotic salinity response
## 910 photomorphogenesis
## 736 aging
## 930 plant-type cell wall organization
## 2889 defense response by callose deposition in cell wall
## 291 'de novo' pyrimidine nucleobase biosynthetic process
## 1173 regulation of stomatal movement
## 2526 lignin catabolic process
## 860 response to water
## 1671 cysteine biosynthetic process
## 2964 membrane organization
## 269 mitochondrial electron transport, NADH to ubiquinone
## 1125 root epidermal cell differentiation
## 2848 proteolysis involved in cellular protein catabolic process
## 516 fatty acid biosynthetic process
## 1380 response to cyclopentenone
## 2831 regulation of monopolar cell growth
## 2214 ribosomal large subunit biogenesis
## 1916 methylation
## 774 biosynthetic process
## 1769 actin filament depolymerization
## ontology over_represented_padjust
## 390 BP 9.525171e-73
## 921 BP 4.103175e-35
## 2575 BP 1.102497e-19
## 2211 BP 4.175470e-17
## 859 BP 4.367163e-17
## 854 BP 1.767360e-16
## 960 BP 3.179527e-13
## 646 BP 1.820070e-12
## 2917 BP 7.486321e-12
## 855 BP 7.486321e-12
## 359 BP 4.749521e-09
## 2088 BP 4.749521e-09
## 958 BP 3.449155e-08
## 419 BP 3.552098e-08
## 178 BP 3.552098e-08
## 2253 BP 9.734226e-08
## 890 BP 1.034233e-07
## 3270 BP 1.146856e-07
## 642 BP 3.099983e-07
## 2239 BP 5.767253e-07
## 1210 BP 1.297807e-06
## 2152 BP 1.426400e-06
## 8 BP 3.210875e-06
## 894 BP 4.781402e-06
## 392 BP 5.911309e-06
## 1008 BP 1.657745e-05
## 2646 BP 1.736964e-05
## 1183 BP 3.042130e-05
## 3708 BP 3.984116e-05
## 972 BP 8.465621e-05
## 2254 BP 1.032654e-04
## 853 BP 1.032654e-04
## 914 BP 1.126956e-04
## 9 BP 1.492940e-04
## 2768 BP 1.836681e-04
## 1327 BP 2.227872e-04
## 557 BP 2.482992e-04
## 973 BP 4.561771e-04
## 967 BP 4.841539e-04
## 952 BP 5.172433e-04
## 1087 BP 5.909668e-04
## 739 BP 7.314829e-04
## 1530 BP 8.242989e-04
## 961 BP 8.984394e-04
## 3255 BP 1.037153e-03
## 2716 BP 1.066264e-03
## 3251 BP 1.199975e-03
## 153 BP 1.278435e-03
## 649 BP 1.450276e-03
## 423 BP 1.536711e-03
## 1737 BP 1.536711e-03
## 898 BP 1.609159e-03
## 2091 BP 1.792842e-03
## 2487 BP 1.793424e-03
## 2913 BP 1.946232e-03
## 594 BP 3.442925e-03
## 1205 BP 4.030348e-03
## 676 BP 4.414116e-03
## 1166 BP 4.769977e-03
## 3252 BP 4.912944e-03
## 3217 BP 4.912944e-03
## 1174 BP 5.443604e-03
## 2196 BP 5.534013e-03
## 607 BP 5.826860e-03
## 2795 BP 5.826860e-03
## 992 BP 6.091719e-03
## 985 BP 6.191689e-03
## 1760 BP 6.191689e-03
## 1001 BP 6.191689e-03
## 3546 BP 6.699672e-03
## 602 BP 6.699888e-03
## 1003 BP 6.711271e-03
## 2241 BP 7.045247e-03
## 452 BP 7.367459e-03
## 957 BP 7.655830e-03
## 87 BP 8.060805e-03
## 2679 BP 8.060805e-03
## 1116 BP 8.060805e-03
## 861 BP 8.060805e-03
## 91 BP 8.698568e-03
## 32 BP 9.515868e-03
## 3747 BP 1.124944e-02
## 2750 BP 1.150378e-02
## 636 BP 1.190998e-02
## 2259 BP 1.875346e-02
## 2973 BP 1.875346e-02
## 26 BP 1.901612e-02
## 1422 BP 2.002254e-02
## 1072 BP 2.046836e-02
## 748 BP 2.197937e-02
## 899 BP 2.197937e-02
## 2908 BP 2.263284e-02
## 897 BP 2.266840e-02
## 1030 BP 2.375186e-02
## 634 BP 2.439172e-02
## 2301 BP 2.445245e-02
## 203 BP 2.606568e-02
## 793 BP 2.634936e-02
## 2486 BP 2.634936e-02
## 1031 BP 2.686840e-02
## 2237 BP 2.702038e-02
## 910 BP 2.713585e-02
## 736 BP 2.735610e-02
## 930 BP 2.825812e-02
## 2889 BP 2.825812e-02
## 291 BP 3.175032e-02
## 1173 BP 3.289993e-02
## 2526 BP 3.488706e-02
## 860 BP 3.617970e-02
## 1671 BP 3.617970e-02
## 2964 BP 3.643942e-02
## 269 BP 3.829442e-02
## 1125 BP 3.843036e-02
## 2848 BP 4.027667e-02
## 516 BP 4.027667e-02
## 1380 BP 4.162793e-02
## 2831 BP 4.485574e-02
## 2214 BP 4.502099e-02
## 1916 BP 4.628279e-02
## 774 BP 4.707152e-02
## 1769 BP 4.877295e-02
write_csv(GO.ORA.temp, path=file.path("..","output","twoafternoon.any.trtlive.DEGs.DEGs.GO.ORA.v3.0anno.csv"))
session info
sessionInfo
## function (package = NULL)
## {
## z <- list()
## z$R.version <- R.Version()
## z$platform <- z$R.version$platform
## if (nzchar(.Platform$r_arch))
## z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
## z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer,
## "-bit)")
## z$locale <- Sys.getlocale()
## z$running <- osVersion
## z$RNGkind <- RNGkind()
## if (is.null(package)) {
## package <- grep("^package:", search(), value = TRUE)
## keep <- vapply(package, function(x) x == "package:base" ||
## !is.null(attr(as.environment(x), "path")), NA)
## package <- .rmpkg(package[keep])
## }
## pkgDesc <- lapply(package, packageDescription, encoding = NA)
## if (length(package) == 0)
## stop("no valid packages were specified")
## basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
## x$Priority == "base")
## z$basePkgs <- package[basePkgs]
## if (any(!basePkgs)) {
## z$otherPkgs <- pkgDesc[!basePkgs]
## names(z$otherPkgs) <- package[!basePkgs]
## }
## loadedOnly <- loadedNamespaces()
## loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
## if (length(loadedOnly)) {
## names(loadedOnly) <- loadedOnly
## pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
## z$loadedOnly <- pkgDesc[loadedOnly]
## }
## z$matprod <- as.character(options("matprod"))
## es <- extSoftVersion()
## z$BLAS <- as.character(es["BLAS"])
## z$LAPACK <- La_library()
## class(z) <- "sessionInfo"
## z
## }
## <bytecode: 0x7fab9925cd98>
## <environment: namespace:utils>